System/Perl/Python Dependencies:

Cutadapt:

pip install cutadapt or easy_install cutadapt

OR if you lack root privs

pip install --user cutadapt or easy_install --user cutadapt

Note: if you install it as a non-root user, you must ensure the install location is on your path, or specify the location of cutadapt with the --cutadapt argument. This is usually in ~/.local/bin/cutadapt, but may vary with your particular distribution.

Bowtie:

This version may not be the latest, visit the official Bowtie website for the latest version